Contacts of the helix formed by residues 57 - 67 (chain D) in PDB entry 1U3H
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 57 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73C LEU* 5.0 0.7 - - - +
76C ARG* 2.7 34.0 + - - -
37D TYR* 3.9 16.5 - - - -
38D LEU* 3.7 15.5 - - + -
54D GLY* 3.3 5.8 + - - +
55D ARG 3.2 2.0 + - - -
56D PRO* 1.3 79.4 - - - +
58D ALA* 1.3 67.9 + - - +
59D GLU 3.5 1.1 - - - -
60D TYR* 3.3 5.7 + - - +
61D TYR* 2.8 45.0 + - + -
7P SER* 3.0 29.6 - - - -
8P GLN 4.1 3.5 + - - -
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Residues in contact with ALA 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D LEU* 4.6 5.0 - - - +
47D TYR 3.7 20.6 - - - +
48D ARG* 5.1 0.9 - - - -
49D ALA* 4.3 17.9 - - + +
54D GLY 3.9 4.2 + - - -
55D ARG 3.9 9.9 + - - +
57D ASP* 1.3 76.0 - - - +
59D GLU* 1.3 62.7 + - - +
61D TYR* 3.2 1.9 + - - +
62D ASN* 2.7 35.5 + - - +
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Residues in contact with GLU 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55D ARG 5.2 1.2 + - - -
56D PRO 5.3 1.5 + - - +
57D ASP 3.5 0.4 - - - -
58D ALA* 1.3 78.5 - - - +
60D TYR* 1.3 64.4 + - - +
62D ASN* 3.1 7.2 + - - +
63D LYS* 3.0 58.8 + - + +
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Residues in contact with TYR 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B ASP* 4.4 9.5 + - - -
56D PRO 4.7 7.8 + - - +
57D ASP* 3.3 9.1 + - - +
59D GLU* 1.3 79.4 - - - +
61D TYR* 1.3 72.8 + + + +
63D LYS* 3.1 17.0 + - + +
64D GLN* 2.9 68.9 + - + +
67D TYR* 3.5 24.9 + + - -
6P PRO 4.0 6.1 - - - -
7P SER 4.3 3.6 + - - -
8P GLN* 3.3 41.3 + - - +
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Residues in contact with TYR 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69C ASN* 3.9 2.9 + - - -
30D TYR* 3.8 16.4 - + - -
37D TYR* 5.0 2.3 + - - -
38D LEU* 3.4 25.1 - - + -
47D TYR* 3.8 29.5 - + + -
57D ASP* 2.8 52.7 + - + +
58D ALA 3.6 3.4 - - - +
60D TYR* 1.3 79.6 - + - +
62D ASN* 1.3 58.1 + - - +
67D TYR* 2.8 48.3 + + - +
68D LEU 3.2 6.2 + - - -
5P ARG* 2.7 38.3 + - + -
6P PRO 3.4 20.5 + - - -
7P SER* 3.5 11.8 + - - -
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Residues in contact with ASN 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D GLU* 3.0 25.4 + - - +
47D TYR* 2.8 44.5 + - - +
58D ALA* 2.7 33.1 + - - +
59D GLU* 3.7 5.9 - - - +
61D TYR* 1.3 75.9 - - - +
63D LYS* 1.3 63.2 + - - +
68D LEU* 3.0 42.3 - - + +
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Residues in contact with LYS 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D GLU* 3.0 57.3 + - + +
60D TYR* 3.1 18.1 + - + +
62D ASN* 1.3 83.5 - - + +
64D GLN* 1.3 71.7 + - + +
67D TYR 3.4 0.9 + - - -
68D LEU 4.4 1.0 + - - -
69D GLU 5.4 1.0 + - - -
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Residues in contact with GLN 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B ASP* 5.6 3.6 + - - +
60D TYR* 2.9 58.7 + - + +
63D LYS* 1.3 86.2 - - + +
67D TYR* 1.3 79.6 + - + +
70D ARG* 3.0 32.7 + - - +
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Residues in contact with TYR 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B ASP* 4.4 6.4 + - - -
104B TYR* 3.4 38.1 - + - -
47D TYR* 3.8 11.7 - - + +
60D TYR* 3.5 16.2 + + - -
61D TYR* 2.8 49.1 + + - +
63D LYS 4.7 0.2 - - - -
64D GLN* 1.3 96.5 - - + +
68D LEU* 1.3 66.5 + - - +
69D GLU 3.1 3.1 - - - -
70D ARG* 2.6 20.6 + - - -
71D THR* 3.0 16.5 + - - +
5P ARG* 3.6 29.6 - - + +
6P PRO* 2.7 41.0 + - + +
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Residues in contact with LEU 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D PHE* 4.0 16.4 - - + -
45D GLY 3.4 23.6 - - - +
46D GLU* 4.3 7.6 - - + +
47D TYR* 4.0 8.6 - - + -
61D TYR 3.2 7.3 + - - -
62D ASN* 3.0 45.6 + - + +
63D LYS 4.4 0.4 + - - -
67D TYR* 1.3 72.4 - - - +
69D GLU* 1.3 62.8 + - - +
71D THR* 3.5 0.5 + - - -
72D ARG* 3.1 52.3 + - - +
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Residues in contact with GLU 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A LEU* 3.4 25.6 - - + +
63D LYS 5.4 1.2 + - - -
67D TYR 2.7 4.8 + - - -
68D LEU* 1.3 78.3 - - - +
70D ARG* 1.3 63.7 + - + +
72D ARG* 3.7 7.8 + - - +
73D ALA* 3.4 22.7 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il